pandomics

DNA analysis scripts and databases

Useful software Tool kit:

• seqtk (Toolkit for processing sequences in FASTA/Q formats): https://github.com/lh3/seqtk

Useful databases and websites for genomics:

• ENdb (experimentally validated enhancer database): http://www.licpathway.net/ENdb/index.php

• HACER (Human Active Enhancer database):http://bioinfo.vanderbilt.edu/AE/HACER/　

• VISTA enhancer database: https://enhancer.lbl.gov/

• EnDisease (database of enhancer - disease): http://bioinfo.au.tsinghua.edu.cn/endisease/

• Jaspar transcription factor motif database: http://jaspar.genereg.net/

• ChIP-Atlas (uniform processed chip-seq data): http://chip-atlas.org/

• ReMap: http://remap.univ-amu.fr/

• TopMed program (https://www.nhlbi.nih.gov/science/trans-omics-precision-medicine-topmed-program) (https://www.nature.com/articles/s41586-021-03205-y)

• Mouse phenotypes (http://www.mousephenotype.org/)

Cancer

• Database for mutational cancer drivers: Integrative OncoGenomics
• Database for cancer dependency screening: https://www.nature.com/articles/s41586-019-1103-9; Pediatric: https://www.nature.com/articles/s41588-021-00819-w
• Gene expression summary for TCGA and GTEx: GEPIA
• cancer genomics mutational resources: cBioPortal

Gene set Enrichment Testing tools

• Enrichr
• DAVID
• GREAT
• GSEA
• LR-path